Is MAP1B p.Ala2332Val (c.6995C>T) pathogenic?

MAP1B p.Ala2332Val (c.6995C>T) is classified Likely benign in MAP1B (ClinVar, Single submitter, 1 submitter; last evaluated 2022-04-13). AlphaMissense: likely benign (0.0619); Very rare (popmax 0.0022%, sas); Associated with Inborn genetic diseases.

What condition is associated with MAP1B p.Ala2332Val (c.6995C>T)?

MAP1B p.Ala2332Val (c.6995C>T) is associated with Inborn genetic diseases (ClinVar).

How common is MAP1B p.Ala2332Val (c.6995C>T) in the general population?

MAP1B p.Ala2332Val (c.6995C>T) is very rare (popmax 0.0022%, sas) (gnomAD).

What do computational predictors say about MAP1B p.Ala2332Val (c.6995C>T)?

AlphaMissense predicts likely benign (score 0.0619) — an in-silico prediction, not a clinical call.

MAP1B p.Ala2332Val

c.6995C>T · rs771129683 · VCV2283852

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0619 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.0022%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0619	likely benign
REVEL	0.028	moderately benign-leaning
SaProt	LLR -6.92	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 -0.1	GERP -4.8, phastCons 0.001
Regional constraint	o/e 0.71	unconstrained · MANE · 5,431 bp · p 1.1e-08 · regional, not allelic
Overall
CADD	0.755	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 0.0022% South Asian · 2/91,002 alleles

Filtering AF 0.000365% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000137%

Overall 0.000248% 4/1,612,974 alleles · very rare exomes 3/1,460,736 · genomes 1/152,238 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0022%	45,501
African / African-American	0.00133%	74,924
European (non-Finnish)	8.48e-05%	1,179,313

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.Ala2332Val
Coding: c.6995C>T
MANE Select: NM_005909
dbSNP: rs771129683
Type: single nucleotide variant
Location: chr5:72200350 (GRCh38)
Gene constraint: LOEUF 0.105 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 46.18
Residue 2332: a UniProt-annotated variant site (in pvnh9); a UniProt-annotated variant site (in pvnh9; no effect on protein expression); the 'disordered' region; the 'mediates interaction with tmem185a' region

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

MAP1B p.Ala2332Ser Likely benign ★ same residue
MAP1B p.Ala966Val Uncertain significance ★★ ⚠ same condition
MAP1B p.Asp1480Tyr Uncertain significance ★★ ⚠ same condition
MAP1B p.Asp1993Gly Uncertain significance ★★ ⚠ same condition
MAP1B p.Glu1944Lys Uncertain significance ★★ ⚠ same condition
MAP1B p.Glu2435Val Uncertain significance ★★ ⚠ same condition
MAP1B p.Gly919Arg Uncertain significance ★★ ⚠ same condition
MAP1B p.Gly932Ser Uncertain significance ★★ ⚠ 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/map1b-p-ala2332val (accessed [today's date]).

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