Is MAP1A p.Lys837Arg (c.2510A>G) pathogenic?

MAP1A p.Lys837Arg (c.2510A>G) is classified Uncertain significance in MAP1A (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-28). AlphaMissense: ambiguous (0.3449); Rare (popmax 0.115%, mid).

How common is MAP1A p.Lys837Arg (c.2510A>G) in the general population?

MAP1A p.Lys837Arg (c.2510A>G) is rare (popmax 0.115%, mid) (gnomAD).

What do computational predictors say about MAP1A p.Lys837Arg (c.2510A>G)?

AlphaMissense predicts ambiguous (score 0.3449) — an in-silico prediction, not a clinical call.

MAP1A p.Lys837Arg

c.2510A>G · rs55904898 · VCV3122662

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3449 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.115%, mid)

Computational evidence

Protein change
AlphaMissense	0.3449	ambiguous
REVEL	0.121	moderately benign-leaning
SaProt	—	not scored · why
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 1.6, phastCons 1
Overall
CADD	25.5	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL is an independent agreement signal.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.115% Middle Eastern · 7/6,062 alleles

Filtering AF 0.0542% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0459%

Overall 0.0208% 336/1,614,066 alleles · rare exomes 291/1,461,804 · genomes 45/152,262 · joint denominator

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.432%	231
Middle Easterngrpmax	0.115%	866
Admixed American	0.0683%	1,464
Remaining individualsnot grpmax-eligible	0.032%	3,125
East Asian	0.0201%	4,987
European (non-Finnish)	0.0107%	9,365
African / African-American	0.00533%	18,755
Finnishnot grpmax-eligible	0.00156%	63,950

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: MAP1A
Protein: p.Lys837Arg
Coding: c.2510A>G
MANE Select: NM_002373
dbSNP: rs55904898
Type: single nucleotide variant
Location: chr15:43523983 (GRCh38)
Structure: AlphaFold pLDDT 94.44 · 41 PDB

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

Similar variants

MAP1A p.Arg2734Gln Uncertain significance ★★ same type
MAP1A p.Gly567Ala Uncertain significance ★★ ⚠ same type
MAP1A p.Gly482= Benign/Likely benign ★★ same type
MAP1A p.Leu1621Val Benign ★★ same type
MAP1A p.Ser1152= Likely benign ★★ same type
MAP1A p.Ser1311= Benign/Likely benign ★★ same type
MAP1A p.Ser1544= Benign ★★ same type
MAP1A p.Ser1858Cys Likely benign ★★ same type

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/map1a-p-lys837arg (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown