Is MAP7 p.Ala615Thr (c.1843G>A) pathogenic?

MAP7 p.Ala615Thr (c.1843G>A) is classified Likely benign in MAP7 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-12-01). AlphaMissense: likely benign (0.0758); Rare (popmax 0.857%, sas).

How common is MAP7 p.Ala615Thr (c.1843G>A) in the general population?

MAP7 p.Ala615Thr (c.1843G>A) is rare (popmax 0.857%, sas) (gnomAD).

What do computational predictors say about MAP7 p.Ala615Thr (c.1843G>A)?

AlphaMissense predicts likely benign (score 0.0758) — an in-silico prediction, not a clinical call.

MAP7 p.Ala615Thr

c.1843G>A · rs147645484 · VCV2656930

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0758 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.857%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0758	likely benign
REVEL	0.044	moderately benign-leaning
SaProt	LLR -5.81	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.099	GERP 2.2, phastCons 0.83
Regional constraint	o/e 0.97	unconstrained · MANE · 206 kb · p 0.43 · regional, not allelic
Overall
CADD	15.62	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 0.857% South Asian · 778/90,810 alleles

Filtering AF 0.807% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.787%

Overall 0.202% 3,267/1,613,504 alleles · rare exomes 3,026/1,461,206 · genomes 241/152,298 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.857%	117
Finnishnot grpmax-eligible	0.603%	166
European (non-Finnish)	0.163%	612
Remaining individualsnot grpmax-eligible	0.162%	619
Middle Eastern	0.149%	673
Admixed American	0.0801%	1,249
African / African-American	0.0213%	4,688
East Asian	0.00223%	44,854

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.Ala615Thr
Coding: c.1843G>A
MANE Select: NM_003980
dbSNP: rs147645484
Type: single nucleotide variant
Location: chr6:136359992 (GRCh38)
Gene constraint: LOEUF 0.749 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 62.72 · 1 PDB
Residue 615: 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-ala615thr (accessed [today's date]).

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