Is MAP1A p.Arg2480Cys (c.7438C>T) pathogenic?

MAP1A p.Arg2480Cys (c.7438C>T) is classified Uncertain significance in MAP1A (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-20). AlphaMissense: likely benign (0.1489); Very rare (popmax 0.00659%, sas).

How common is MAP1A p.Arg2480Cys (c.7438C>T) in the general population?

MAP1A p.Arg2480Cys (c.7438C>T) is very rare (popmax 0.00659%, sas) (gnomAD).

What do computational predictors say about MAP1A p.Arg2480Cys (c.7438C>T)?

AlphaMissense predicts likely benign (score 0.1489) — an in-silico prediction, not a clinical call.

MAP1A p.Arg2480Cys

c.7438C>T · VCV4102979

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1489 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00659%, sas)

Computational evidence

Protein change
AlphaMissense	0.1489	likely benign
REVEL	0.299	indeterminate
SaProt	—	not scored · why
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6	GERP 1.8, phastCons 1
Overall
CADD	22.2	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 0.00659% South Asian · 6/91,080 alleles

Filtering AF 0.00286% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00195%

Overall 0.00149% 24/1,612,748 alleles · very rare exomes 21/1,460,742 · genomes 3/152,006 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00659%	15,180
African / African-American	0.00267%	37,431
European (non-Finnish)	0.00136%	73,743

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.Arg2480Cys
Coding: c.7438C>T
MANE Select: NM_002373
Type: single nucleotide variant
Location: chr15:43528911 (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.Arg2480His Uncertain significance ★ ⚠ same residue
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

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-arg2480cys (accessed [today's date]).

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