Is SLMAP p.Ala310= (c.930A>G) pathogenic?

SLMAP p.Ala310= (c.930A>G) is classified Likely benign in SLMAP (ClinVar, Single submitter, 1 submitter; last evaluated 2023-01-05). Very rare (popmax 0.00805%, afr).

How common is SLMAP p.Ala310= (c.930A>G) in the general population?

SLMAP p.Ala310= (c.930A>G) is very rare (popmax 0.00805%, afr) (gnomAD).

SLMAP p.Ala310=

c.930A>G · rs112767112 · VCV2448002

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00805%, afr)

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 -1.1	GERP -5
Overall
CADD	4.703	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00805% African / African-American · 6/74,564 alleles

Filtering AF 0.00348% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00239%

Overall 0.000566% 9/1,591,470 alleles · very rare exomes 7/1,439,140 · genomes 2/152,330 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00805%	12,427
Remaining individualsnot grpmax-eligible	0.00162%	61,722
European (non-Finnish)	0.000172%	579,885

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: SLMAP
Protein: p.Ala310=
Coding: c.930A>G
MANE Select: NM_001377540
dbSNP: rs112767112
Type: single nucleotide variant
Location: chr3:57862050 (GRCh38)
Gene constraint: LOEUF 0.531 · pLI 0.86 (gnomAD)
Structure: AlphaFold pLDDT 77.74 · 3 PDB

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

Similar variants

SLMAP p.Ala310Thr Uncertain significance ★ ⚠ same residue
SLMAP p.Ala310Val Uncertain significance ★ ⚠ same residue
SLMAP c.*38C>T Uncertain significance ★★ ⚠ same type
SLMAP c.*55G>A Uncertain significance ★★ ⚠ same type
SLMAP c.*70G>A Uncertain significance ★★ ⚠ same type
SLMAP p.Ala365Asp Uncertain significance ★★ ⚠ same type
SLMAP p.Ala506Ser Uncertain significance ★★ ⚠ same type
SLMAP p.Ala597Val 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/slmap-p-ala310 (accessed [today's date]).

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