MAP1A — 435 ClinVar variants

All ClinVar germline MAP1A variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 344 flagged for review →

1 Pathogenic · 1 Conflicting · 3 Benign · 2 Benign/Likely benign · 28 Likely benign · 400 Uncertain significance

Full MAP1A gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 344

Variants where the independent computational evidence doesn't line up with the clinical picture — a QC signal for a second look, not a reclassification.

Predictors agree, ClinVar conflicts 1

ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.

MAP1A p.Gly1914Arg Conflicting Single submitter

Predictors lean, ClinVar uncertain 321

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification. · showing the 150 best-reviewed of 321

Predictors split 22

The independent predictors disagree with each other — read with care.

All MAP1A variants

Pathogenic 1

p.Met1829fs Single submitter neurodevelopmental disorder

Conflicting classifications of pathogenicity 1

p.Gly1914Arg Single submitter ⚠

Benign 3

p.Leu1621Val Multiple submitters
p.Ser1544= Multiple submitters
p.Ser2664Gly Single submitter

Benign/Likely benign 2

p.Gly482= Multiple submitters
p.Ser1311= Multiple submitters

Likely benign 28

p.Ser1152= Multiple submitters
p.Ser1858Cys Multiple submitters
p.Ser2152= Multiple submitters
p.Ala1308Val Single submitter
p.Ala1670Thr Single submitter
p.Ala2272= Single submitter
p.Arg1483Lys Single submitter
p.Arg2445Cys Single submitter
p.Asn1078Ser Single submitter
p.Asn2379Lys Single submitter
p.Asp673Glu Single submitter
p.Gly2418Ala Single submitter
p.Leu1153Phe Single submitter
p.Leu2563Ile Single submitter
p.Met1103Arg Single submitter
p.Met2053Val Single submitter
p.Met994Thr Single submitter ⚠
p.Pro2423Ser Single submitter
p.Pro2636= Single submitter
p.Pro783= Single submitter
p.Ser121= Single submitter
p.Ser1299Leu Single submitter
p.Ser695Gly Single submitter
p.Val596Ile Single submitter
p.Arg2574His No assertion criteria MAP1A-related disorder
p.Asn1078Lys No assertion criteria MAP1A-related disorder
p.Pro2370= No assertion criteria MAP1A-related disorder
p.Tyr773Cys No assertion criteria MAP1A-related disorder

Uncertain significance 400

Showing the top 300 by review status; the full set is in the sitemap.

p.Arg2734Gln Multiple submitters MAP1A-related disorder
p.Gly567Ala Multiple submitters ⚠
p.Ala1290Ser Single submitter ⚠
p.Ala1633Ser Single submitter ⚠
p.Ala1633Thr Single submitter ⚠
p.Ala1717Pro Single submitter ⚠
p.Ala173Thr Single submitter ⚠
p.Ala1855Ser Single submitter ⚠
p.Ala1888Thr Single submitter ⚠
p.Ala2037Asp Single submitter ⚠
p.Ala2061Val Single submitter ⚠
p.Ala2122Gly Single submitter ⚠
p.Ala2165Val Single submitter
p.Ala2272Val Single submitter ⚠
p.Ala2282Val Single submitter ⚠
p.Ala2312Val Single submitter ⚠
p.Ala2377Thr Single submitter ⚠
p.Ala2383Val Single submitter ⚠
p.Ala2527Val Single submitter ⚠
p.Ala325Val Single submitter ⚠
p.Ala345Pro Single submitter ⚠
p.Ala348Thr Single submitter ⚠
p.Ala640Thr Single submitter ⚠
p.Ala674Thr Single submitter ⚠
p.Ala674Val Single submitter ⚠
p.Ala786Asp Single submitter ⚠
p.Ala790Gly Single submitter ⚠
p.Arg1035Cys Single submitter ⚠
p.Arg1035Leu Single submitter ⚠
p.Arg1068Ser Single submitter ⚠
p.Arg1123Lys Single submitter ⚠
p.Arg1139Ser Single submitter ⚠
p.Arg1139Thr Single submitter ⚠
p.Arg1185Cys Single submitter ⚠
p.Arg1272Gln Single submitter ⚠
p.Arg150Gln Single submitter ⚠
p.Arg154Pro Single submitter
p.Arg1634Thr Single submitter ⚠
p.Arg1657Gly Single submitter ⚠
p.Arg1704Gln Single submitter ⚠
p.Arg1704Trp Single submitter ⚠
p.Arg1718Gly Single submitter ⚠
p.Arg1725Gln Single submitter ⚠
p.Arg1743Gln Single submitter ⚠
p.Arg1743Trp Single submitter ⚠
p.Arg1748Trp Single submitter ⚠
p.Arg1771His Single submitter ⚠
p.Arg1790Cys Single submitter ⚠
p.Arg1790His Single submitter ⚠
p.Arg1910Leu Single submitter ⚠
p.Arg197Gln Single submitter ⚠
p.Arg2009Gln Single submitter ⚠
p.Arg2098Trp Single submitter ⚠
p.Arg2115Gln Single submitter ⚠
p.Arg2115Leu Single submitter ⚠
p.Arg2158Gln Single submitter ⚠
p.Arg2187Cys Single submitter ⚠
p.Arg2274His Single submitter ⚠
p.Arg2390His Single submitter ⚠
p.Arg2402Trp Single submitter ⚠
p.Arg2442Trp Single submitter ⚠
p.Arg2445Leu Single submitter ⚠
p.Arg2472Trp Single submitter ⚠
p.Arg2479Gln Single submitter ⚠
p.Arg2479Trp Single submitter ⚠
p.Arg2480Cys Single submitter
p.Arg2480His Single submitter ⚠
p.Arg2481Trp Single submitter ⚠
p.Arg2569His Single submitter ⚠
p.Arg2574Cys Single submitter ⚠
p.Arg2574Gly Single submitter
p.Arg2594Lys Single submitter ⚠
p.Arg2596Trp Single submitter ⚠
p.Arg2608Gly Single submitter ⚠
p.Arg2620Gln Single submitter ⚠
p.Arg2621Cys Single submitter
p.Arg2625Gln Single submitter ⚠
p.Arg2628His Single submitter ⚠
p.Arg2639Gln Single submitter ⚠
p.Arg2642Trp Single submitter ⚠
p.Arg2648Cys Single submitter ⚠
p.Arg2714Gln Single submitter
p.Arg284Gln Single submitter ⚠
p.Arg290His Single submitter
p.Arg337Gln Single submitter ⚠
p.Arg337Trp Single submitter ⚠
p.Arg349His Single submitter ⚠
p.Arg449Ser Single submitter ⚠
p.Arg472His Single submitter
p.Arg493Cys Single submitter ⚠
p.Arg493His Single submitter ⚠
p.Arg540Leu Single submitter ⚠
p.Arg550Lys Single submitter ⚠
p.Arg762Cys Single submitter ⚠
p.Arg762His Single submitter ⚠
p.Arg767Ser Single submitter ⚠
p.Arg767Thr Single submitter ⚠
p.Arg879Cys Single submitter
p.Asn1231Lys Single submitter ⚠
p.Asn167His Single submitter ⚠
p.Asn1831Ser Single submitter ⚠
p.Asn233Ser Single submitter ⚠
p.Asn257Ser Single submitter ⚠
p.Asn2779Ser Single submitter ⚠
p.Asn56Ser Single submitter
p.Asp1080Asn Single submitter ⚠
p.Asp1371Val Single submitter ⚠
p.Asp1384Val Single submitter ⚠
p.Asp1419Glu Single submitter ⚠
p.Asp1426Tyr Single submitter ⚠
p.Asp1433Val Single submitter ⚠
p.Asp1527Asn Single submitter ⚠
p.Asp1541Gly Single submitter ⚠
p.Asp1735Glu Single submitter ⚠
p.Asp1757His Single submitter ⚠
p.Asp2107Gly Single submitter ⚠
p.Asp2151Gly Single submitter ⚠
p.Asp2327Tyr Single submitter ⚠
p.Asp2330Gly Single submitter ⚠
p.Asp2404Asn Single submitter ⚠
p.Asp2465Ala Single submitter ⚠
p.Asp2532Asn Single submitter
p.Asp298Asn Single submitter
p.Asp556Asn Single submitter ⚠
p.Asp80Glu Single submitter ⚠
p.Cys1702Ser Single submitter ⚠
p.Cys1983Arg Single submitter ⚠
p.Cys2339Trp Single submitter ⚠
p.Gln1166Lys Single submitter ⚠
p.Gln1537Glu Single submitter ⚠
p.Gln1577Arg Single submitter ⚠
p.Gln1629Arg Single submitter ⚠
p.Gln1759His Single submitter ⚠
p.Gln1953Glu Single submitter ⚠
p.Gln2435Arg Single submitter ⚠
p.Gln315Glu Single submitter ⚠
p.Gln574His Single submitter ⚠
p.Glu1017Gly Single submitter ⚠
p.Glu1047Val Single submitter ⚠
p.Glu111Lys Single submitter
p.Glu1220Lys Single submitter ⚠
p.Glu1244Lys Single submitter ⚠
p.Glu1378Lys Single submitter ⚠
p.Glu1392Lys Single submitter ⚠
p.Glu1444Ter Single submitter
p.Glu1465Gln Single submitter ⚠
p.Glu1517Lys Single submitter ⚠
p.Glu1531Lys Single submitter ⚠
p.Glu1580Lys Single submitter ⚠
p.Glu1703Asp Single submitter
p.Glu1760Ala Single submitter ⚠
p.Glu1770Val Single submitter
p.Glu1919Gly Single submitter ⚠
p.Glu1947Lys Single submitter ⚠
p.Glu2014Asp Single submitter
p.Glu2219_Lys2222del Single submitter MAP1A-related disorder
p.Glu2257Gln Single submitter ⚠
p.Glu2273Gln Single submitter ⚠
p.Glu2288Lys Single submitter ⚠
p.Glu2410Val Single submitter ⚠
p.Glu338Gly Single submitter ⚠
p.Glu360Gly Single submitter ⚠
p.Glu455Gly Single submitter
p.Glu587Gly Single submitter ⚠
p.Glu624Asp Single submitter ⚠
p.Glu643Asp Single submitter ⚠
p.Glu712Lys Single submitter ⚠
p.Glu822Ala Single submitter
p.Glu935Asp Single submitter ⚠
p.Glu940Asp Single submitter ⚠
p.Glu942Lys Single submitter ⚠
p.Glu942Val Single submitter ⚠
p.Gly100Arg Single submitter
p.Gly100Glu Single submitter
p.Gly1038fs Single submitter
p.Gly1110Arg Single submitter ⚠
p.Gly1238Glu Single submitter ⚠
p.Gly1307Glu Single submitter ⚠
p.Gly1733Ala Single submitter ⚠
p.Gly1779Val Single submitter ⚠
p.Gly1920Asp Single submitter ⚠
p.Gly1980Ser Single submitter ⚠
p.Gly2008Ser Single submitter ⚠
p.Gly2113Arg Single submitter
p.Gly2207Glu Single submitter ⚠
p.Gly2420Arg Single submitter ⚠
p.Gly2421Ser Single submitter ⚠
p.Gly582Arg Single submitter ⚠
p.Gly604Arg Single submitter ⚠
p.Gly679Arg Single submitter ⚠
p.Gly701Asp Single submitter ⚠
p.Gly777Arg Single submitter ⚠
p.Gly799Ala Single submitter ⚠
p.His1248Arg Single submitter ⚠
p.His1259Arg Single submitter ⚠
p.His165Pro Single submitter
p.His2336Tyr Single submitter ⚠
p.His2444Arg Single submitter ⚠
p.His2558Gln Single submitter ⚠
p.His2701Asp Single submitter ⚠
p.His665Asn Single submitter ⚠
p.His684Leu Single submitter ⚠
p.His684Tyr Single submitter ⚠
p.His825fs Single submitter
p.Ile1340Val Single submitter ⚠
p.Ile1569Val Single submitter ⚠
p.Ile1795Leu Single submitter
p.Ile2068Met Single submitter ⚠
p.Ile229Thr Single submitter
p.Ile927Thr Single submitter ⚠
p.Leu1197His Single submitter
p.Leu1197Pro Single submitter ⚠
p.Leu1408Val Single submitter ⚠
p.Leu166Phe Single submitter
p.Leu1780Val Single submitter ⚠
p.Leu1905Arg Single submitter
p.Leu2077Phe Single submitter ⚠
p.Leu545Phe Single submitter ⚠
p.Leu546Val Single submitter ⚠
p.Leu634Phe Single submitter ⚠
p.Leu854fs Single submitter
p.Leu901Val Single submitter ⚠
p.Lys1096Arg Single submitter ⚠
p.Lys1341Asn Single submitter ⚠
p.Lys1434Thr Single submitter ⚠
p.Lys1441Asn Single submitter ⚠
p.Lys1547Glu Single submitter ⚠
p.Lys1561Glu Single submitter ⚠
p.Lys1610Asn Single submitter ⚠
p.Lys1933Glu Single submitter ⚠
p.Lys2376Gln Single submitter ⚠
p.Lys2614Gln Single submitter MAP1A-related disorder ⚠
p.Lys297Asn Single submitter ⚠
p.Lys320Glu Single submitter
p.Lys437Arg Single submitter ⚠
p.Lys450Arg Single submitter ⚠
p.Lys453fs Single submitter
p.Lys591Arg Single submitter ⚠
p.Lys837Arg Single submitter
p.Lys905Arg Single submitter ⚠
p.Lys908Arg Single submitter ⚠
p.Met1103Thr Single submitter ⚠
p.Met1241Thr Single submitter ⚠
p.Met1253Thr Single submitter ⚠
p.Met1607Thr Single submitter ⚠
p.Met1826Ile Single submitter ⚠
p.Met1826Leu Single submitter ⚠
p.Met1829Thr Single submitter ⚠
p.Met590Arg Single submitter ⚠
p.Met994Val Single submitter ⚠
p.Phe137Leu Single submitter ⚠
p.Phe2350Leu Single submitter
p.Phe2452Val Single submitter ⚠
p.Phe768Cys Single submitter ⚠
p.Pro1003Ser Single submitter ⚠
p.Pro1051Leu Single submitter ⚠
p.Pro1147Ser Single submitter ⚠
p.Pro1187Ser Single submitter ⚠
p.Pro1362Leu Single submitter ⚠
p.Pro1382Arg Single submitter ⚠
p.Pro1382Leu Single submitter ⚠
p.Pro1511Leu Single submitter ⚠
p.Pro1593fs Single submitter
p.Pro1660Leu Single submitter ⚠
p.Pro1763Arg Single submitter ⚠
p.Pro1781fs Single submitter
p.Pro1851His Single submitter ⚠
p.Pro1851Thr Single submitter ⚠
p.Pro1854Ala Single submitter ⚠
p.Pro1854Thr Single submitter ⚠
p.Pro1861Ser Single submitter ⚠
p.Pro1925Ala Single submitter ⚠
p.Pro1958Thr Single submitter ⚠
p.Pro1981Ser Single submitter ⚠
p.Pro2020Leu Single submitter ⚠
p.Pro2051Ser Single submitter ⚠
p.Pro2064Arg Single submitter
p.Pro2076Ala Single submitter ⚠
p.Pro2164Leu Single submitter
p.Pro2177Ser Single submitter ⚠
p.Pro2208Leu Single submitter ⚠
p.Pro2208Ser Single submitter ⚠
p.Pro2209Thr Single submitter ⚠
p.Pro2253Leu Single submitter ⚠
p.Pro2266Leu Single submitter ⚠
p.Pro2311Ser Single submitter ⚠
p.Pro2372Leu Single submitter ⚠
p.Pro2422Leu Single submitter ⚠
p.Pro2423Leu Single submitter ⚠
p.Pro2443Thr Single submitter ⚠
p.Pro2450Leu Single submitter
p.Pro2456Ser Single submitter ⚠
p.Pro2485Leu Single submitter ⚠
p.Pro2516Arg Single submitter ⚠
p.Pro2632Leu Single submitter ⚠
p.Pro374Ser Single submitter ⚠
p.Pro481Leu Single submitter ⚠
p.Pro502Ala Single submitter ⚠
p.Pro600Arg Single submitter ⚠
p.Pro759Leu Single submitter ⚠