Is MAP4 p.Val613Met (c.1837G>A) pathogenic?

MAP4 p.Val613Met (c.1837G>A) is classified Likely benign in MAP4 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-02-22). AlphaMissense: likely benign (0.0783); Rare (popmax 0.876%, afr); Associated with MAP4-related disorder.

What condition is associated with MAP4 p.Val613Met (c.1837G>A)?

MAP4 p.Val613Met (c.1837G>A) is associated with MAP4-related disorder (ClinVar).

How common is MAP4 p.Val613Met (c.1837G>A) in the general population?

MAP4 p.Val613Met (c.1837G>A) is rare (popmax 0.876%, afr) (gnomAD).

What do computational predictors say about MAP4 p.Val613Met (c.1837G>A)?

AlphaMissense predicts likely benign (score 0.0783) — an in-silico prediction, not a clinical call.

MAP4 p.Val613Met

c.1837G>A · rs78150694 · VCV3034981

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0783 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.876%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

MAP4-related disorder

Computational evidence

Protein change
AlphaMissense	0.0783	likely benign
REVEL	0.077	moderately benign-leaning
SaProt	LLR -7.08	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -0.005	GERP 0.63
Regional constraint	o/e 0.91	unconstrained · MANE · 123 kb · p 2.5e-05 · regional, not allelic
Overall
CADD	6.743	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 0.876% African / African-American · 658/75,074 alleles

Filtering AF 0.821% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.799%

Overall 0.0538% 868/1,613,964 alleles · rare exomes 492/1,461,606 · genomes 376/152,358 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.876%	114
Middle Eastern	0.0825%	1,212
Remaining individualsnot grpmax-eligible	0.08%	1,250
Admixed American	0.0733%	1,364
European (non-Finnish)	0.00932%	10,726
South Asian	0.0011%	91,016

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: MAP4
Protein: p.Val613Met
Coding: c.1837G>A
MANE Select: NM_001385682
dbSNP: rs78150694
Type: single nucleotide variant
Location: chr3:47915990 (GRCh38)
Gene constraint: LOEUF 0.512 · pLI 0.14 (gnomAD)
Structure: AlphaFold pLDDT 43.03

Full MAP4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

MAP4-related disorder

Similar variants

MAP4 c.292+2409G>A Likely benign same condition
MAP4 c.*100G>A Likely benign same condition
MAP4 c.*44G>A Likely benign same condition
MAP4 p.Ala2123= Likely benign same condition
MAP4 p.Ala2134= Likely benign same condition
MAP4 p.Ala437= Likely benign same condition
MAP4 p.Arg23Gln Benign same condition
MAP4 p.Arg23Trp Likely benign ⚠ same condition

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/map4-p-val613met (accessed [today's date]).

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