Is MAP7 p.Arg71Trp (c.211C>T) pathogenic?

MAP7 p.Arg71Trp (c.211C>T) is classified Uncertain significance in MAP7 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-10-06). AlphaMissense: likely pathogenic (0.8025); Ultra-rare (popmax 0.0498%, mid).

How common is MAP7 p.Arg71Trp (c.211C>T) in the general population?

MAP7 p.Arg71Trp (c.211C>T) is ultra-rare (popmax 0.0498%, mid) (gnomAD).

What do computational predictors say about MAP7 p.Arg71Trp (c.211C>T)?

AlphaMissense predicts likely pathogenic (score 0.8025) — an in-silico prediction, not a clinical call.

MAP7 p.Arg71Trp

c.211C>T · rs138281942 · VCV2204323

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8025 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0498%, mid)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.8025	likely pathogenic
REVEL	0.197	benign-leaning
SaProt	LLR -13.31	damaging
⇒ AlphaMissense and SaProt call this damaging; REVEL does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.2	GERP 1.6, phastCons 1
Regional constraint	o/e 0.97	unconstrained · MANE · 206 kb · p 0.43 · regional, not allelic
Overall
CADD	25.2	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 0.0498% Middle Eastern · 3/6,020 alleles

Filtering AF 0.0142% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0113%

Overall 0.0122% 191/1,565,548 alleles · ultra-rare exomes 174/1,413,592 · genomes 17/151,956 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0498%	2,007
Remaining individualsnot grpmax-eligible	0.0248%	4,038
Admixed American	0.0241%	4,147
European (non-Finnish)	0.013%	7,693
East Asian	0.0095%	10,528
African / African-American	0.00408%	24,509
South Asian	0.00352%	28,421

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.Arg71Trp
Coding: c.211C>T
MANE Select: NM_003980
dbSNP: rs138281942
Type: single nucleotide variant
Location: chr6:136411653 (GRCh38)
Gene constraint: LOEUF 0.749 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 62.72 · 1 PDB
Residue 71: the 'disordered' region

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

Similar variants

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
MAP7 p.Ala17Val 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-arg71trp (accessed [today's date]).

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