Is MAP1B p.Val962Ile (c.2884G>A) pathogenic?

MAP1B p.Val962Ile (c.2884G>A) is classified Benign in MAP1B (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-06-01). AlphaMissense: likely benign (0.0641); Rare (popmax 0.936%, afr).

How common is MAP1B p.Val962Ile (c.2884G>A) in the general population?

MAP1B p.Val962Ile (c.2884G>A) is rare (popmax 0.936%, afr) (gnomAD).

What do computational predictors say about MAP1B p.Val962Ile (c.2884G>A)?

AlphaMissense predicts likely benign (score 0.0641) — an in-silico prediction, not a clinical call.

MAP1B p.Val962Ile

c.2884G>A · rs35796057 · VCV746831

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.0641 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.936%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0641	likely benign
REVEL	0.012	strongly benign-leaning
SaProt	LLR -7.07	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 1.1	GERP -2.9, phastCons 0.15
Regional constraint	o/e 0.91	unconstrained · MANE · 5,330 bp · p 1.3e-05 · regional, not allelic
Overall
CADD	2.328	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 0.936% African / African-American · 702/75,020 alleles

Filtering AF 0.878% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.856%

Overall 0.056% 903/1,613,844 alleles · rare exomes 508/1,461,560 · genomes 395/152,284 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.936%	107
Admixed American	0.0716%	1,396
Remaining individualsnot grpmax-eligible	0.0656%	1,524
Middle Eastern	0.0344%	2,911
European (non-Finnish)	0.00941%	10,631
South Asian	0.00439%	22,765

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: MAP1B
Protein: p.Val962Ile
Coding: c.2884G>A
MANE Select: NM_005909
dbSNP: rs35796057
Type: single nucleotide variant
Location: chr5:72196239 (GRCh38)
Gene constraint: LOEUF 0.105 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 46.18
Residue 962: the 'disordered' region; a UniProt-annotated variant site (in pvnh9)

Full MAP1B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

MAP1B p.Val962Leu Uncertain significance ★ ⚠ same residue
MAP1B p.Arg1664Ter Pathogenic/Likely pathogenic ★★ same type
MAP1B p.Arg2140Ter Pathogenic ★★ same type
MAP1B p.Arg303Ter Pathogenic/Likely pathogenic ★★ same type
MAP1B p.Arg85Ter Pathogenic/Likely pathogenic ★★ same type
MAP1B p.Arg999Ter Pathogenic/Likely pathogenic ★★ same type
MAP1B p.Ala966Val Uncertain significance ★★ ⚠ same type
MAP1B p.Arg1399Cys 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/map1b-p-val962ile (accessed [today's date]).

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