Is CLIP1 p.Met3Val (c.7A>G) pathogenic?

CLIP1 p.Met3Val (c.7A>G) is classified Uncertain significance in CLIP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2017-01-31). AlphaMissense: likely benign (0.0676); Rare (popmax 0.235%, amr).

How common is CLIP1 p.Met3Val (c.7A>G) in the general population?

CLIP1 p.Met3Val (c.7A>G) is rare (popmax 0.235%, amr) (gnomAD).

What do computational predictors say about CLIP1 p.Met3Val (c.7A>G)?

AlphaMissense predicts likely benign (score 0.0676) — an in-silico prediction, not a clinical call.

CLIP1 p.Met3Val

c.7A>G · rs140092191 · VCV434788

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0676 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.235%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0676	likely benign
REVEL	0.151	moderately benign-leaning
SaProt	LLR -5.94	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 -1.6	GERP -0.8
Regional constraint	o/e 0.97	unconstrained · MANE · 2,584 bp · p 0.82 · regional, not allelic
Overall
CADD	8.005	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.235% Admixed American · 140/59,616 alleles

Filtering AF 0.203% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.191%

Overall 0.11% 1,774/1,610,882 alleles · rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.235%	426
European (non-Finnish)	0.13%	769
Remaining individualsnot grpmax-eligible	0.122%	821
African / African-American	0.0214%	4,679
Ashkenazi Jewishnot grpmax-eligible	0.0203%	4,922
Middle Eastern	0.0165%	6,054
Finnishnot grpmax-eligible	0.00469%	21,313
South Asian	0.0011%	90,778

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: CLIP1
Protein: p.Met3Val
Coding: c.7A>G
MANE Select: NM_001247997
dbSNP: rs140092191
Type: single nucleotide variant
Location: chr12:122380446 (GRCh38)
Gene constraint: LOEUF 0.455 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 72.16 · 11 PDB

Full CLIP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CLIP1 p.Ala142Val Uncertain significance ★★ ⚠ same type
CLIP1 p.Arg342Cys Uncertain significance ★★ ⚠ same type
CLIP1 p.Gly1356Arg Uncertain significance ★★ ⚠ same type
CLIP1 p.Lys1267Arg Uncertain significance ★★ ⚠ same type
CLIP1 p.Ala1224Ser Likely benign ★★ same type
CLIP1 p.Ala301= Benign ★★ same type
CLIP1 p.Asn99= Benign/Likely benign ★★ same type
CLIP1 p.Lys851= Likely benign ★★ 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/clip1-p-met3val (accessed [today's date]).

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