Is COL15A1 p.Phe91= (c.273C>T) pathogenic?

COL15A1 p.Phe91= (c.273C>T) is classified Likely benign in COL15A1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-06-18). Rare (popmax 0.151%, afr); Associated with COL15A1-related disorder.

What condition is associated with COL15A1 p.Phe91= (c.273C>T)?

COL15A1 p.Phe91= (c.273C>T) is associated with COL15A1-related disorder (ClinVar).

How common is COL15A1 p.Phe91= (c.273C>T) in the general population?

COL15A1 p.Phe91= (c.273C>T) is rare (popmax 0.151%, afr) (gnomAD).

COL15A1 p.Phe91=

c.273C>T · rs141708640 · VCV3033343

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.151%, afr)

Conditions

COL15A1-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 -15	GERP -3.6
Overall
CADD	0.331	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.151% African / African-American · 113/75,072 alleles

Filtering AF 0.128% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.12%

Overall 0.00787% 127/1,614,202 alleles · rare exomes 71/1,461,810 · genomes 56/152,392 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.151%	664
Admixed American	0.005%	20,012
Remaining individualsnot grpmax-eligible	0.0032%	31,256
South Asian	0.0011%	91,092
European (non-Finnish)	0.000678%	147,506

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: COL15A1
Protein: p.Phe91=
Coding: c.273C>T
MANE Select: NM_001855
dbSNP: rs141708640
Type: single nucleotide variant
Location: chr9:98985737 (GRCh38)
Gene constraint: LOEUF 0.763 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 54.68 · 1 PDB
Residue 91: the laminin g-like domain

Full COL15A1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

COL15A1-related disorder

Similar variants

COL15A1 c.100+9C>A Likely benign same condition
COL15A1 c.1761+6A>G Benign same condition
COL15A1 c.1762-6T>C Benign same condition
COL15A1 c.1762-9T>C Likely benign same condition
COL15A1 c.3402+10A>G Likely benign same condition
COL15A1 c.952+9G>A Benign same condition
COL15A1 p.Ala1148= Likely benign same condition
COL15A1 p.Ala1148Val 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/col15a1-p-phe91 (accessed [today's date]).

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