NLGN3[gene] - ClinVar - NCBI

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	Variation	Gene (Protein Change)	Type (Consequence)	Condition	Classification, Review status
Select item 488014	Single allele	ARSF, CFAP47 +2632 more	Duplication	Autism +1 more	GPathogenic
Select item 146764	GRCh38/hg38 Xp22.33-q28(chrX:10001-156030895)x1	ABCB7, ABCD1 +2634 more	Copy number loss	See cases	GPathogenic
Select item 160983	GRCh38/hg38 Xp22.33-q28(chrX:10679-156013167)x1	LOC130067918, LOC130067919 +2633 more	Copy number loss	See cases	GPathogenic
Select item 160897	GRCh38/hg38 Xp22.33-q28(chrX:10679-156022206)x3	LOC130068528, LOC130068529 +2634 more	Copy number gain	See cases	GPathogenic
Select item 160890	GRCh38/hg38 Xp22.33-q28(chrX:10679-156022206)x1	ARMCX5, ARMCX5-GPRASP2 +2634 more	Copy number loss	See cases	GPathogenic
Select item 148051	GRCh38/hg38 Xp22.33-q13.3(chrX:10679-76420505)x3	LOC130068369, LOC130068370 +1399 more	Copy number gain	See cases	GPathogenic
Select item 144172	GRCh38/hg38 Xp22.33-q28(chrX:10679-156022826)x4	APOO, APOOL +2634 more	Copy number gain	See cases	GPathogenic
Select item 57087	GRCh38/hg38 Xp22.33-q28(chrX:10679-156022206)x1	LOC130068308, LOC130068309 +2634 more	Copy number loss	See cases	GPathogenic
Select item 57086	GRCh38/hg38 Xp22.33-q28(chrX:10679-156022206)x3	ABCB7, ABCD1 +2634 more	Copy number gain	See cases	GPathogenic
Select item 154558	GRCh38/hg38 Xp22.33-q28(chrX:10701-156003229)x3	LOC126863325, LOC126863326 +2633 more	Copy number gain	See cases	GPathogenic
Select item 150510	GRCh38/hg38 Xp22.33-q21.31(chrX:10701-88318651)x1	LOC130067920, LOC130067921 +1476 more	Copy number loss	See cases	GPathogenic
Select item 148821	GRCh38/hg38 Xp22.33-q22.3(chrX:10701-106113403)x1	LOC126863242, LOC126863243 +1629 more	Copy number loss	See cases	GPathogenic
Select item 146861	GRCh38/hg38 Xp22.33-q28(chrX:10701-156003229)x1	LOC130068075, LOC130068076 +2633 more	Copy number loss	See cases	GPathogenic
Select item 146857	GRCh38/hg38 Xp22.33-q25(chrX:10701-128393708)	LOC130068153, LOC130068154 +1933 more	Copy number loss	See cases	GPathogenic
Select item 144465	GRCh38/hg38 Xp22.33-q28(chrX:10701-156003242)x1	LOC130068278, LOC130068279 +2633 more	Copy number loss	See cases	GPathogenic
Select item 144429	GRCh38/hg38 Xp22.33-q28(chrX:10701-156003242)x3	LOC130068310, LOC130068311 +2633 more	Copy number gain	See cases	GPathogenic
Select item 144310	GRCh38/hg38 Xp22.33-q28(chrX:10701-155978689)x1	VAMP7, VBP1 +2632 more	Copy number loss	See cases	GPathogenic
Select item 161089	GRCh38/hg38 Xp22.33-q28(chrX:14245-155999293)x1	ABCB7, ABCD1 +2633 more	Copy number loss	See cases	GPathogenic
Select item 57161	GRCh38/hg38 Xp22.33-q28(chrX:20140-155699618)x1	LOC107988022, LOC107988024 +2629 more	Copy number loss	See cases	GPathogenic
Select item 57160	GRCh38/hg38 Xp22.33-q28(chrX:20140-155699618)x3	LOC130067944, LOC130067945 +2629 more	Copy number gain	See cases	GPathogenic
Select item 152900	GRCh38/hg38 Xp22.33-q28(chrX:20297-156016920)x3	ABCB7, ABCD1 +2634 more	Copy number gain	See cases	GPathogenic
Select item 145995	GRCh38/hg38 Xp22.33-q28(chrX:20297-156026127)x1	ABCB7, ABCD1 +2634 more	Copy number loss	See cases	GPathogenic
Select item 145162	GRCh38/hg38 Xp22.33-q28(chrX:20297-155999253)x3	LOC130067929, LOC130067930 +2633 more	Copy number gain	See cases	GPathogenic
Select item 58553	GRCh38/hg38 Xp22.33-q28(chrX:26101-155999293)x3	LOC130068219, LOC130068220 +2633 more	Copy number gain	See cases	GPathogenic
Select item 161091	GRCh38/hg38 Xp22.33-q28(chrX:26102-155996431)x3	ABCB7, ABCD1 +2632 more	Copy number gain	See cases	GPathogenic
Select item 161088	GRCh38/hg38 Xp22.33-q28(chrX:26102-155996431)x1	VAMP7, VBP1 +2632 more	Copy number loss	See cases	GPathogenic
Select item 58555	GRCh38/hg38 Xp22.33-q28(chrX:27245-155996431)x3	LOC126863224, LOC126863225 +2632 more	Copy number gain	See cases	GPathogenic
Select item 147257	GRCh38/hg38 Xp22.33-q28(chrX:40904-155998166)x1	LOC121627971, LOC121627972 +2633 more	Copy number loss	See cases	GPathogenic
Select item 155374	GRCh38/hg38 Xp22.33-q28(chrX:251879-156004066)x1	FUNDC1, FUNDC2 +2633 more	Copy number loss	See cases	GPathogenic
Select item 155366	GRCh38/hg38 Xp22.33-q28(chrX:251879-156004066)x3	LOC126863244, LOC126863245 +2633 more	Copy number gain	See cases	GPathogenic
Select item 153937	GRCh38/hg38 Xp22.33-q24(chrX:251879-118847157)x3	MAGED2, MAGED4 +1799 more	Copy number gain	See cases	GPathogenic
Select item 155152	GRCh38/hg38 Xp22.33-q28(chrX:251880-156004066)x3	ABCB7, ABCD1 +2633 more	Copy number gain	See cases	GPathogenic
Select item 152158	GRCh38/hg38 Xp22.33-q28(chrX:251880-156004066)x1	LOC130068098, LOC130068099 +2633 more	Copy number loss	See cases	Gconflicting data from submitters
Select item 152157	GRCh38/hg38 Xp22.33-q28(chrX:251880-156004066)x4	ABCB7, ABCD1 +2633 more	Copy number gain	See cases	GPathogenic
Select item 151130	GRCh38/hg38 Xp22.33-q28(chrX:251880-156004181)x3	LOC126863315, LOC126863316 +2633 more	Copy number gain	See cases	GPathogenic
Select item 59200	GRCh38/hg38 Xp22.33-q22.1(chrX:675360-100368517)x1	LOC125467739, LOC125467740 +1494 more	Copy number loss	See cases	GPathogenic
Select item 150422	GRCh38/hg38 Xp22.33-q28(chrX:1085618-155699644)x1	LOC130068055, LOC130068056 +2612 more	Copy number loss	See cases	GPathogenic
Select item 152899	GRCh38/hg38 Xp22.33-q28(chrX:2299223-155992188)x3	CNKSR2, COL4A5 +2604 more	Copy number gain	See cases	GPathogenic
Select item 3242589	GRCh38/hg38 Xp22.33-q28(chrX:2757837-156030895)x2	LOC130068417, LOC130068418 +2599 more	Copy number gain	Klinefelter syndrome	GPathogenic
Select item 147627	GRCh38/hg38 Xp22.33-q28(chrX:2765636-155522304)x3	LOC130068152, LOC130068153 +2594 more	Copy number gain	See cases	GPathogenic
Select item 147683	GRCh38/hg38 Xp22.33-q28(chrX:2782275-155611794)x2	LOC130068468, LOC130068469 +2594 more	Copy number gain	See cases	GPathogenic
Select item 58586	GRCh38/hg38 Xp22.33-q28(chrX:2790845-155699618)x3	LOC130067984, LOC130067985 +2596 more	Copy number gain	See cases	GPathogenic
Select item 57225	GRCh38/hg38 Xp22.33-q28(chrX:3092486-155699618)x2	ABCB7, ABCD1 +2586 more	Copy number gain	See cases	GPathogenic
Select item 149705	GRCh38/hg38 Xp22.2-q27.3(chrX:13020141-143473520)x1	ABCB7, ACE2 +2047 more	Copy number loss	See cases	GPathogenic
Select item 146240	GRCh38/hg38 Xp21.1-q28(chrX:36237706-156022206)x1	LOC130068242, LOC130068243 +2103 more	Copy number loss	See cases	GPathogenic
Select item 145974	GRCh38/hg38 Xp21.1-q28(chrX:37076284-156016920)x1	LOC126863280, LOC126863281 +2099 more	Copy number loss	See cases	GPathogenic
Select item 148340	GRCh38/hg38 Xp11.23-q22.1(chrX:49100536-102174742)x1	IGBP1, IL2RG +640 more	Copy number loss	See cases	GPathogenic
Select item 153303	GRCh38/hg38 Xp11.22-q24(chrX:50289384-119297604)	LOC130068457, LOC130068458 +824 more	Copy number loss	See cases	GPathogenic
Select item 155282	GRCh38/hg38 Xp11.22-q28(chrX:53144751-156003242)x1	P2RY10, P2RY4 +1590 more	Copy number loss	See cases	GPathogenic
Select item 145980	GRCh38/hg38 Xp11.22-q21.31(chrX:53985575-92203108)x1	HDAC8, HDX +410 more	Copy number loss	See cases	GPathogenic
Select item 155064	GRCh38/hg38 Xp11.21-q13.3(chrX:56431359-76557419)x1	ABCB7, AMER1 +269 more	Copy number loss	See cases	GPathogenic
Select item 57923	GRCh38/hg38 Xp11.21-q28(chrX:57372584-155996431)x1	ABCB7, ABCD1 +1476 more	Copy number loss	See cases	GPathogenic
Select item 148479	GRCh38/hg38 Xq11.1-28(chrX:62561604-156003242)x3	ABCB7, ABCD1 +1467 more	Copy number gain	See cases	GPathogenic
Select item 150589	GRCh38/hg38 Xq11.1-28(chrX:62712219-156003242)x3	LOC130068612, LOC130068613 +1467 more	Copy number gain	See cases	GPathogenic
Select item 145167	GRCh38/hg38 Xq11.1-21.1(chrX:62712219-78605009)x3	ABCB7, AMER1 +263 more	Copy number gain	See cases	GPathogenic
Select item 144543	GRCh38/hg38 Xq11.1-28(chrX:62712230-155978888)x3	LOC126863288, LOC126863289 +1466 more	Copy number gain	See cases	GPathogenic
Select item 57924	GRCh38/hg38 Xq11.1-28(chrX:63279794-155939524)x1	LOC130068438, LOC130068439 +1464 more	Copy number loss	See cases	GPathogenic
Select item 2663780	NC_000023.11:g.(?_66445907)_(78172208_?)dup	ABCB7, AR +206 more	Duplication	Xq13q21 duplication	GPathogenic
Select item 154251	GRCh38/hg38 Xq12-21.1(chrX:66445907-78172208)x3	ABCB7, AR +206 more	Copy number gain	See cases	GPathogenic
Select item 58640	GRCh38/hg38 Xq12-21.1(chrX:67621041-76868590)x2	FTX, GCNA +175 more	Copy number gain	See cases	GPathogenic
Select item 58641	GRCh38/hg38 Xq12-13.3(chrX:68382004-75243150)x2	ABCB7, ARR3 +161 more	Copy number gain	See cases	GPathogenic
Select item 146778	GRCh38/hg38 Xq13.1(chrX:70974174-71207055)x2	CXorf65, FOXO4 +15 more	Copy number gain	See cases	GUncertain significance
Select item 155458	GRCh38/hg38 Xq13.1(chrX:71022322-71682982)x2	LOC130068418, LOC130068419 +44 more	Copy number gain	See cases	GUncertain significance
Select item 155235	GRCh38/hg38 Xq13.1(chrX:71071787-71777197)x2	CXCR3, CXorf49 +45 more	Copy number gain	See cases	GUncertain significance
Select item 588054	NM_181303.2(NLGN3):c.-5G>A	NLGN3	Single nucleotide variant (5 prime UTR variant +1 more)	Inborn genetic diseases	GUncertain significance
Select item 2412926	NM_181303.2(NLGN3):c.2T>G (p.Met1Arg)	NLGN3 (M1R)	Single nucleotide variant (missense variant +2 more)	not provided	GUncertain significance
Select item 425503	NM_181303.2(NLGN3):c.10C>T (p.Arg4Trp)	NLGN3 (R4W)	Single nucleotide variant (missense variant +1 more)	not provided +2 more	GConflicting classifications of pathogenicity
Select item 195351	NM_181303.2(NLGN3):c.20C>T (p.Pro7Leu)	NLGN3 (P7L)	Single nucleotide variant (missense variant +1 more)	not provided	GUncertain significance
Select item 436018	NM_181303.2(NLGN3):c.21G>A (p.Pro7=)	NLGN3	Single nucleotide variant (synonymous variant +1 more)	not specified	GLikely benign
Select item 929068	NM_181303.2(NLGN3):c.26C>T (p.Ser9Leu)	NLGN3 (S9L)	Single nucleotide variant (missense variant +1 more)	not specified	GUncertain significance
Select item 918125	NM_181303.2(NLGN3):c.38G>A (p.Ser13Asn)	NLGN3 (S13N)	Single nucleotide variant (missense variant +1 more)	not specified	GUncertain significance
Select item 1743952	NM_181303.2(NLGN3):c.48C>T (p.Pro16=)	NLGN3	Single nucleotide variant (synonymous variant +1 more)	Inborn genetic diseases	GLikely benign
Select item 589123	NM_181303.2(NLGN3):c.51G>A (p.Thr17=)	NLGN3	Single nucleotide variant (synonymous variant +1 more)	Inborn genetic diseases	GLikely benign
Select item 2580694	NM_181303.2(NLGN3):c.93G>C (p.Leu31Phe)	NLGN3 (L31F)	Single nucleotide variant (missense variant +1 more)	not provided	GUncertain significance
Select item 1767897	NM_181303.2(NLGN3):c.96G>A (p.Ala32=)	NLGN3	Single nucleotide variant (synonymous variant +1 more)	Inborn genetic diseases	GLikely benign
Select item 3383654	NM_181303.2(NLGN3):c.139C>T (p.His47Tyr)	NLGN3 (H47Y)	Single nucleotide variant (missense variant +1 more)	not provided	GUncertain significance
Select item 2689590	NM_181303.2(NLGN3):c.146G>A (p.Gly49Glu)	NLGN3 (G49E)	Single nucleotide variant (missense variant +1 more)	not provided	GUncertain significance
Select item 2428992	NM_181303.2(NLGN3):c.160G>A (p.Ala54Thr)	NLGN3 (A54T)	Single nucleotide variant (missense variant +1 more)	not provided	GUncertain significance
Select item 2442803	NM_181303.2(NLGN3):c.163C>T (p.Arg55Ter)	NLGN3 (R55*)	Single nucleotide variant (nonsense +1 more)	Autism, susceptibility to, X-linked 1	GUncertain significance
Select item 978847	NM_181303.2(NLGN3):c.163C>G (p.Arg55Gly)	NLGN3 (R55G)	Single nucleotide variant (missense variant +1 more)	Intellectual disability	GUncertain significance
Select item 1048954	NM_181303.2(NLGN3):c.170C>T (p.Pro57Leu)	NLGN3 (P57L)	Single nucleotide variant (missense variant +1 more)	Inborn genetic diseases	GUncertain significance
Select item 3370144	NM_181303.2(NLGN3):c.171del (p.Leu58fs)	NLGN3 (L58fs)	Deletion (frameshift variant +1 more)	not provided	GUncertain significance
Select item 2502772	NM_181303.2(NLGN3):c.178A>G (p.Ser60Gly)	NLGN3 (S60G)	Single nucleotide variant (missense variant +1 more)	not provided	GUncertain significance
Select item 3343376	NM_181303.2(NLGN3):c.184A>G (p.Ile62Val)	NLGN3 (I62V)	Single nucleotide variant (missense variant +1 more)	not provided	GUncertain significance
Select item 520912	NM_181303.2(NLGN3):c.214dup (p.Val72fs)	NLGN3 (V72fs)	Duplication (frameshift variant +1 more)	Inborn genetic diseases	GPathogenic
Select item 1788074	NM_181303.2(NLGN3):c.222C>T (p.Tyr74=)	NLGN3	Single nucleotide variant (synonymous variant +1 more)	Inborn genetic diseases	GLikely benign
Select item 1806786	NM_181303.2(NLGN3):c.226G>A (p.Ala76Thr)	NLGN3 (A76T)	Single nucleotide variant (missense variant +1 more)	not provided	GUncertain significance
Select item 1789226	NM_181303.2(NLGN3):c.229C>T (p.Pro77Ser)	NLGN3 (P77S)	Single nucleotide variant (missense variant +1 more)	Inborn genetic diseases	GUncertain significance
Select item 2691361	NM_181303.2(NLGN3):c.237C>G (p.Ile79Met)	NLGN3 (I79M)	Single nucleotide variant (missense variant +1 more)	not specified	GUncertain significance
Select item 2391251	NM_181303.2(NLGN3):c.241G>A (p.Glu81Lys)	NLGN3 (E81K)	Single nucleotide variant (missense variant +1 more)	Inborn genetic diseases	GUncertain significance
Select item 975303	NM_181303.2(NLGN3):c.244A>C (p.Lys82Gln)	NLGN3 (K82Q)	Single nucleotide variant (missense variant +1 more)	Intellectual disability	GLikely benign
Select item 1305145	NM_181303.2(NLGN3):c.247C>T (p.Arg83Cys)	NLGN3 (R83C)	Single nucleotide variant (missense variant +1 more)	not provided	GUncertain significance
Select item 3030662	NM_181303.2(NLGN3):c.253C>G (p.Leu85Val)	NLGN3 (L85V)	Single nucleotide variant (missense variant +1 more)	NLGN3-related disorder	GUncertain significance
Select item 2660854	NM_181303.2(NLGN3):c.255G>T (p.Leu85=)	NLGN3	Single nucleotide variant (synonymous variant +1 more)	not provided	GUncertain significance
Select item 95926	NM_181303.2(NLGN3):c.282G>A (p.Ser94=)	NLGN3	Single nucleotide variant (synonymous variant +1 more)	not provided +1 more	GConflicting classifications of pathogenicity
Select item 3200429	NM_181303.2(NLGN3):c.307C>A (p.Pro103Thr)	NLGN3 (P103T)	Single nucleotide variant (missense variant +1 more)	Inborn genetic diseases	GUncertain significance
Select item 2660855	NM_181303.2(NLGN3):c.342G>A (p.Val114=)	NLGN3	Single nucleotide variant (synonymous variant +1 more)	not provided	GUncertain significance
Select item 3373595	NM_181303.2(NLGN3):c.353T>C (p.Met118Thr)	NLGN3 (M118T +1 more)	Single nucleotide variant (missense variant +1 more)	not provided	GUncertain significance
Select item 2443311	NM_181303.2(NLGN3):c.366G>A (p.Trp122Ter)	NLGN3 (W122* +1 more)	Single nucleotide variant (nonsense)	Hypogonadotropic hypogonadism	GPathogenic
Select item 2660856	NM_181303.2(NLGN3):c.388G>A (p.Val130Ile)	NLGN3 (V130I +1 more)	Single nucleotide variant (missense variant)	not provided	GUncertain significance

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