Is MAP7 p.Arg77Gln (c.230G>A) pathogenic?

MAP7 p.Arg77Gln (c.230G>A) is classified Uncertain significance in MAP7 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-08-14). AlphaMissense: likely benign (0.1913); Ultra-rare (popmax 0.0346%, nfe).

How common is MAP7 p.Arg77Gln (c.230G>A) in the general population?

MAP7 p.Arg77Gln (c.230G>A) is ultra-rare (popmax 0.0346%, nfe) (gnomAD).

What do computational predictors say about MAP7 p.Arg77Gln (c.230G>A)?

AlphaMissense predicts likely benign (score 0.1913) — an in-silico prediction, not a clinical call.

MAP7 p.Arg77Gln

c.230G>A · rs141805814 · VCV2401132

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1913 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0346%, nfe)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1913	likely benign
REVEL	0.132	moderately benign-leaning
SaProt	LLR -12.18	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.8	GERP 1.6, phastCons 1
Regional constraint	o/e 0.97	unconstrained · MANE · 206 kb · p 0.43 · regional, not allelic
Overall
CADD	24.3	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0346% European (non-Finnish) · 399/1,151,718 alleles

Filtering AF 0.0318% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0307%

Overall 0.0267% 417/1,561,212 alleles · ultra-rare exomes 398/1,409,162 · genomes 19/152,050 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0346%	2,887
Remaining individualsnot grpmax-eligible	0.0132%	7,554
African / African-American	0.0123%	8,151
South Asian	0.00118%	84,864

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: MAP7
Protein: p.Arg77Gln
Coding: c.230G>A
MANE Select: NM_003980
dbSNP: rs141805814
Type: single nucleotide variant
Location: chr6:136411634 (GRCh38)
Gene constraint: LOEUF 0.749 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 62.72 · 1 PDB
Residue 77: the 'disordered' region

Full MAP7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

MAP7 p.Arg77Trp Uncertain significance ★ ⚠ same residue
MAP7 p.Arg214Cys Uncertain significance ★★ ⚠ same type
MAP7 c.1274-1G>C Uncertain significance ★ same type
MAP7 c.67+24403G>A Uncertain significance ★ same type
MAP7 c.67+24406A>G Uncertain significance ★ same type
MAP7 c.67+24434G>T Uncertain significance ★ same type
MAP7 c.752-21T>C Uncertain significance ★ same type
MAP7 c.752-6G>A Uncertain significance ★ 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/map7-p-arg77gln (accessed [today's date]).

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