Is CLUAP1 p.Ala107Val (c.320C>T) pathogenic?

CLUAP1 p.Ala107Val (c.320C>T) is classified Benign in CLUAP1 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-02-02). AlphaMissense: likely pathogenic (0.8422); Common (popmax 18.6%, eas) — too common for a highly-penetrant pathogenic allele.

What do computational predictors say about CLUAP1 p.Ala107Val (c.320C>T)?

AlphaMissense predicts likely pathogenic (score 0.8422) — an in-silico prediction, not a clinical call.

CLUAP1 p.Ala107Val

Q: How common is CLUAP1 p.Ala107Val (c.320C>T) in the general population?

CLUAP1 p.Ala107Val (c.320C>T) is common (popmax 18.6%, eas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.320C>T · rs79133712 · VCV1167691

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely pathogenic

0.8422 · ACMG-weighted

gnomAD v4.1

Common

common (popmax 18.6%, eas) — too common for a highly-penetrant pathogenic allele

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.8422	likely pathogenic
REVEL	0.488	indeterminate
SaProt	LLR -10.49	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 2, phastCons 1
Regional constraint	o/e 1.04	unconstrained · MANE · 35 kb · p 0.32 · regional, not allelic
Overall
CADD	27.5	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 18.6% East Asian · 8,207/44,054 alleles

Filtering AF 18.3% ClinGen BA1/BS1 input FAF95, joint · FAF99 18.2%

Overall 1.33% 21,265/1,602,368 alleles · common

Ancestry group	Frequency	1 in
East Asiangrpmax	18.6%	5
Admixed American	4.89%	20
South Asian	4.01%	25
African / African-American	1.96%	51
Remaining individualsnot grpmax-eligible	1.56%	64
Middle Eastern	1.55%	64
Ashkenazi Jewishnot grpmax-eligible	1.23%	81
Finnishnot grpmax-eligible	0.324%	309
European (non-Finnish)	0.313%	319

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: CLUAP1
Protein: p.Ala107Val
Coding: c.320C>T
MANE Select: NM_015041
dbSNP: rs79133712
Type: single nucleotide variant
Location: chr16:3508389 (GRCh38)
Gene constraint: LOEUF 1.23 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 78.02

Full CLUAP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CLUAP1 p.Ala107Ser Uncertain significance ★ ⚠ same residue
CLUAP1 p.Ala152Glu Uncertain significance ★★ ⚠ same type
CLUAP1 p.Ala188Gly Uncertain significance ★★ ⚠ same type
CLUAP1 p.Ala339Thr Uncertain significance ★★ ⚠ same type
CLUAP1 p.Arg20Gln Uncertain significance ★★ ⚠ same type
CLUAP1 p.Arg228Gln Uncertain significance ★★ ⚠ same type
CLUAP1 p.Arg304His Uncertain significance ★★ ⚠ same type
CLUAP1 p.Arg332Gln 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/cluap1-p-ala107val (accessed [today's date]).

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