Is SURF1 p.Ala5= (c.15T>G) pathogenic?

SURF1 p.Ala5= (c.15T>G) is classified Likely benign in SURF1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2022-05-01). No allele count reported in gnomAD v4.1 (AN 1,413,238).

How common is SURF1 p.Ala5= (c.15T>G) in the general population?

SURF1 p.Ala5= (c.15T>G) is no allele count reported in gnomAD v4.1 (AN 1,413,238) (gnomAD).

SURF1 p.Ala5=

c.15T>G · rs1180014887 · VCV633442

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,413,238)

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 -3.1	GERP -1.6
Overall
CADD	5.084	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,413,238). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: SURF1
Protein: p.Ala5=
Coding: c.15T>G
MANE Select: NM_003172
dbSNP: rs1180014887
Type: single nucleotide variant
Location: chr9:133356439 (GRCh38)
Gene constraint: LOEUF 1.559 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 82.62

Full SURF1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

SURF1 p.Ala5Pro Uncertain significance ★ ⚠ same residue
SURF1 c.106+1G>C Likely pathogenic ★★ same type
SURF1 c.240+1G>T Pathogenic ★★ same type
SURF1 c.324-11T>G Pathogenic/Likely pathogenic ★★ same type
SURF1 c.516-1G>A Pathogenic ★★ same type
SURF1 c.516-2A>G Pathogenic ★★ same type
SURF1 c.588+1G>C Pathogenic ★★ same type
SURF1 c.751+1G>A Pathogenic ★★ 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/surf1-p-ala5 (accessed [today's date]).

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