Is ITGA8 p.Phe57= (c.171C>T) pathogenic?

ITGA8 p.Phe57= (c.171C>T) is classified Likely benign in ITGA8 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2023-12-13). Rare (popmax 0.157%, afr); Associated with ITGA8-related disorder.

What condition is associated with ITGA8 p.Phe57= (c.171C>T)?

ITGA8 p.Phe57= (c.171C>T) is associated with ITGA8-related disorder (ClinVar).

How common is ITGA8 p.Phe57= (c.171C>T) in the general population?

ITGA8 p.Phe57= (c.171C>T) is rare (popmax 0.157%, afr) (gnomAD).

ITGA8 p.Phe57=

c.171C>T · rs145157492 · VCV3034217

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.157%, afr)

Conditions

ITGA8-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.2	GERP 0.31, phastCons 1
Overall
CADD	13.9	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.157% African / African-American · 111/70,676 alleles

Filtering AF 0.133% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.124%

Overall 0.00838% 131/1,562,404 alleles · rare exomes 65/1,410,052 · genomes 66/152,352 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.157%	637
Middle Eastern	0.0169%	5,922
Remaining individualsnot grpmax-eligible	0.0116%	8,620
Admixed American	0.00791%	12,639
South Asian	0.00356%	28,053
European (non-Finnish)	0.00043%	232,377

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: ITGA8
Protein: p.Phe57=
Coding: c.171C>T
MANE Select: NM_003638
dbSNP: rs145157492
Type: single nucleotide variant
Location: chr10:15719601 (GRCh38)
Gene constraint: LOEUF 0.801 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 85.08

Full ITGA8 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ITGA8-related disorder

Similar variants

ITGA8 p.Gln876Ter Likely pathogenic ★★ same condition
ITGA8 p.Arg952Ter Pathogenic ★ same condition
ITGA8 p.Met498Leu Uncertain significance ★ ⚠ same condition
ITGA8 p.Arg594Ter Pathogenic same condition
ITGA8 p.Tyr56Ter Uncertain significance same condition
ITGA8 c.2638-6T>G Likely benign same condition
ITGA8 p.Arg7= Likely benign same condition
ITGA8 p.Phe276= Likely benign 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/itga8-p-phe57 (accessed [today's date]).

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