Is MAP1B p.His51Pro (c.152A>C) pathogenic?

MAP1B p.His51Pro (c.152A>C) is classified Uncertain significance in MAP1B (ClinVar, Single submitter, 1 submitter; last evaluated 2026-08-05). AlphaMissense: likely pathogenic (0.6218); Absent from gnomAD v4.1.

How common is MAP1B p.His51Pro (c.152A>C) in the general population?

MAP1B p.His51Pro (c.152A>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about MAP1B p.His51Pro (c.152A>C)?

AlphaMissense predicts likely pathogenic (score 0.6218) — an in-silico prediction, not a clinical call.

MAP1B p.His51Pro

c.152A>C · rs758951016 · VCV3253535

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.6218 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Computational evidence

Protein change
AlphaMissense	0.6218	likely pathogenic
REVEL	0.361	indeterminate
SaProt	LLR -8.99	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 5.6, phastCons 1
Regional constraint	o/e 0.70	unconstrained · MANE · 87 kb · p 3.4e-10 · regional, not allelic
Overall
CADD	26.7	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: MAP1B
Protein: p.His51Pro
Coding: c.152A>C
MANE Select: NM_005909
dbSNP: rs758951016
Type: single nucleotide variant
Location: chr5:72107683 (GRCh38)
Gene constraint: LOEUF 0.105 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 46.18

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

Similar variants

MAP1B p.His51Tyr 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-his51pro (accessed [today's date]).

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