ISCA1 p.Val6=
c.18C>A · rs1331175531 · VCV1641506
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00545%, 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 3 | GERP 0.047, phastCons 1 |
| Overall | ||
| CADD | 11.84 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00545%
African / African-American · 4/73,330 alleles
Filtering AF
0.0036%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00326%
Overall
0.00373%
58/1,554,340 alleles · very rare
exomes 55/1,402,096 · genomes 3/152,244 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00545% | 18,333 |
| European (non-Finnish) | 0.00461% | 21,680 |
| Remaining individualsnot grpmax-eligible | 0.00166% | 60,236 |
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
- ISCA1
- Protein
- p.Val6=
- Coding
- c.18C>A
- MANE Select
- NM_030940
- dbSNP
- rs1331175531
- Type
- single nucleotide variant
- Location
- chr9:86282441 (GRCh38)
- Gene constraint
- LOEUF 1.785 · pLI 0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.18
Similar variants
- ISCA1 c.241+92G>A Benign ★★ same type
- ISCA1 p.Asn116= Benign ★★ same type
- ISCA1 p.Val111= Likely benign ★★ same type
- ISCA1 p.Ala31Thr Uncertain significance ★ ⚠ same type
- ISCA1 p.Ala8Ser Uncertain significance ★ ⚠ same type
- ISCA1 p.Arg7Pro Uncertain significance ★ ⚠ same type
- ISCA1 p.Arg83Lys Uncertain significance ★ ⚠ same type
- ISCA1 p.Arg83Ser 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/isca1-p-val6 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown